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Mauricio Martinez edited this page Oct 17, 2019 · 60 revisions

Project

{
  "tpn": "TPN:000000001",
  "assignmentStatusName": "Assigned",
  "externalReference": null,
  "withdrawn": false,
  "recovery": false,
  "comment": null,
  "_links": {
    "production_plans": {
      "href": "http://127.0.0.1:8080/api/plans/PIN:0000000001"
    }
  },
  "assignmentStatusStamps": [
    {
      "statusName": "Assigned",
      "date": "2018-02-21T01:15:12.086781"
    }
  ],
  "intentionsByGene": [
    {
      "gene": {
        "name": "Armadillo Repeat Containing 9",
        "symbol": "Armc9",
        "speciesName": "Mus musculus",
        "externalLink": null,
        "accessionId": "MGI:1926045"
      },
      "intention": {
        "alleleTypeName": "Null",
        "molecularMutationTypeName": "Point Mutation",
        "alleleCategorizations": []
      }
    },
    {
      "gene": {
        "name": "RIKEN cDNA 1700030K09 gene",
        "symbol": "1700030K09Rik",
        "speciesName": "Mus musculus",
        "externalLink": null,
        "accessionId": "MGI:1919504"
      },
      "intention": {
        "alleleTypeName": "Null",
        "molecularMutationTypeName": "Point Mutation",
        "alleleCategorizations": [
          {
            "name": "Conditional Ready",
            "description": null
          },
          {
            "name": "Null Reporter",
            "description": null
          }
        ]
      }
    },
    {
      "gene": {
        "name": "ATRX, chromatin remodeler",
        "symbol": "Atrx",
        "speciesName": "Mus musculus",
        "externalLink": null,
        "accessionId": "MGI:103067"
      },
      "intention": {
        "alleleTypeName": "Null",
        "molecularMutationTypeName": "Point Mutation",
        "alleleCategorizations": []
      }
    }
  ],
  "intentionsByLocation": [
    {
      "chrFeatureTypeName": "gene",
      "index": 0,
      "location": {
        "chr": "X",
        "start": 123,
        "stop": 145,
        "strand": null,
        "genomeBuild": null,
        "strain": null,
        "speciesName": "Mus musculus",
        "speciesTaxonId": null
      },
      "intention": {
        "alleleTypeName": "Gain-of-function",
        "molecularMutationTypeName": "Insertion",
        "alleleCategorizations": [
          {
            "name": "Conditional Ready",
            "description": null
          },
          {
            "name": "Null Reporter",
            "description": null
          }
        ]
      }
    },
    {
      "chrFeatureTypeName": "gene",
      "index": 1,
      "location": {
        "chr": "X",
        "start": 423,
        "stop": 545,
        "strand": null,
        "genomeBuild": null,
        "strain": null,
        "speciesName": "Mus musculus",
        "speciesTaxonId": null
      },
      "intention": {
        "alleleTypeName": "Gain-of-function",
        "molecularMutationTypeName": "Insertion",
        "alleleCategorizations": []
      }
    }
  ],
  "intentionsBySequence": [
    {
      "index": 0,
      "sequence": {
        "sequence": "ACTTTGACTATTCTATATTCCTCTGG",
        "sequenceCategoryName": "intention target sequence",
        "typeName": "complete",
        "sequenceLocations": [
          {
            "locationIndex": 0,
            "location": {
              "chr": "X",
              "start": 123,
              "stop": 145,
              "strand": null,
              "genomeBuild": null,
              "strain": null,
              "speciesName": "Mus musculus",
              "speciesTaxonId": null
            }
          },
          {
            "locationIndex": 1,
            "location": {
              "chr": "X",
              "start": 423,
              "stop": 545,
              "strand": null,
              "genomeBuild": null,
              "strain": null,
              "speciesName": "Mus musculus",
              "speciesTaxonId": null
            }
          }
        ]
      },
      "intention": {
        "alleleTypeName": "Null",
        "molecularMutationTypeName": "Insertion",
        "alleleCategorizations": []
      }
    },
    {
      "index": 1,
      "sequenceAttributes": {
        "sequence": "TGAGGACTAGTCTATATCTGGTTCC",
        "sequenceCategoryName": "original starting sequence",
        "typeName": "partial",
        "sequenceLocations": []
      },
      "intention": {
        "alleleTypeName": "Null",
        "molecularMutationTypeName": "Insertion",
        "alleleCategorizations": []
      }
    }
  ],
  "isActive": true,
  "privacyName": "restricted",
  "speciesAttributes": [],
  "consortiaNames": [
    "CMG"
  ]
}

Plan

The Plan object includes attempt information. The attempt section has a different structure depending on the type of attempt. It can be crispr, es-cell, breeding, etc.

Plan with a Crispr Attempt (crispr_attempt_attributes)

{
  "id": 16420,
  "pin": "PIN:000016420",
  "tpn": "TPN:00000001",
  "funder_name": "",
  "work_unit_name": "UCD",
  "is_active": true,
  "status_name": "Production completed",
  "status_dates": [
    {
      "name": "Micro-injection in progress",
      "date": "2014-12-18"
    },
    {
      "name": "Founder obtained",
      "date": "2015-01-06"
    },
    {
      "name": "Chimeras/Founder obtained",
      "date": "2015-01-06"
    },
    {
      "name": "Production complete",
      "date": "2015-02-16"
    }
  ],
  // TODO relation between attempt, outcome, colony
  "comment": null,
  "products_available_for_general_public": true,
  "type": "production",
  "attempt_type_name": "mutagenesis_crispr",
  "crispr_attempt_attributes": {
    "plan_id": 18098,
    "imits_mi_attempt_id": 14903,
    "mi_date": "2014-12-18",
    "attempt_external_ref": "Gpr68 Cas9 Low",
    "experimental": false,
    "comment": "Cas9: 20 ng/ul;\r\ngRNA1: 2.5 ng/ul;\r\ngRNA2: 2.5 ng/ul.\r\nGPRR\r\n",
    "mutagenesis_external_ref": "MF-16",
    "delivery_type_method_name": "Cytoplasmic Injection",
    "voltage": null,
    "number_of_pulses": null,
    "nucleases_attributes": [
      {
        "id": 1,
        "crispr_attempt_plan_id": 18098,
        "concentration": 20,
        "type_name": "CAS9",
        "type_class_name": ""
      }
    ],
    "guides_attributes": [
      {
        "id": 2296,
        "crispr_attempt_plan_id": 18098,
        "chr": "10",
        "stop": 115478571,
        "grna_concentration": null,
        "sequence": "AGGCCGCTGAAACAGCTGGGTGG",
        "start": 115478549,
        "truncated_guide": false,
        "strand": "",
        "genome_build": "",
        "pam3": "",
        "pam5": "",
        "protospacer_sequence": ""
      }
    ],
    "mutagenesis_donors_attributes": [
      {
        "id": 22,
        "crispr_attempt_plan_id": 18098,
        "vector_name": "Afmid-Tm1cshort",
        "concentration": "20",
        "preparation": "Circular",
        "oligo_sequence_fa": ""
      }
    ],
    "reagents_attributes": [
      {
        "id": "",
        "crispr_attempt_plan_id": 18098,
        "name": "",
        "concentration": "",
        "description": ""
      }
    ],
    "genotype_primers_attributes": [
      {
        "id": 1017,
        "crispr_attempt_plan_id": 18098,
        "genomic_end_coordinate": 115478165,
        "genomic_start_coordinate": 115478146,
        "name": "Forward",
        "sequence": "GGGGCTTTTTGACCTTTGTA"
      }
    ],
    "total_embryos_injected": 100,
    "total_embryos_survived": 85,
    "embryo_transfer_day": "Same Day",
    "embryo_2_cell": null,
    "total_transfered": 85,
    "num_founder_pups": 30,
    "assay_attributes": {
      "id": "",
      "crispr_attempt_plan_id": 18098,
      "type_name": "PCR",
      "founder_num_assays": 30,
      "num_deletion_g0_mutants": 14,
      "num_g0_where_mutation_detected": 14,
      "num_hdr_g0_mutants": null,
      "num_hdr_g0_mutants_all_donors_inserted": null,
      "num_hdr_g0_mutants_subset_donors_inserted": null,
      "num_hr_g0_mutants": null,
      "num_nhej_g0_mutants": null
    },
    "num_founders_selected_for_breeding": 2,
    "strain_injected_attributes": {
      "name": "C57BL/6N",
      "mgi_strain_acc_id": "MGI:2159965"
    },
    "outcomes_count": 3
  }
}

Plan with a Breeding Attempt (breeding_attempt_attributes)

{
  "id": 16420,
  "pin": "PIN:000016420",
  "tpn": "TPN:00000001",
  "funder_name": "",
  "work_unit_name": "UCD",
  "is_active": true,
  "status_name": "Production completed",
  "status_dates": [
    {
      "name": "Micro-injection in progress",
      "date": "2014-12-18"
    },
    {
      "name": "Founder obtained",
      "date": "2015-01-06"
    },
    {
      "name": "Chimeras/Founder obtained",
      "date": "2015-01-06"
    },
    {
      "name": "Production complete",
      "date": "2015-02-16"
    }
  ],
  // TODO relation between attempt, outcome, colony
  "comment": null,
  "products_available_for_general_public": true,
  "type": "production",
  "attempt_type_name": "breeding",
  "breeding_attempt_attributes": {
    "plan_id": 18098,
    "imits_mi_mouse_allele_mod_id": 14903,
    "number_of_cre_matings_started": "",
    "number_of_cre_matings_successful": "",
    "cre_excesion": false,
    "tat_cre": false,
    "deleter_strain_attributes": {
      "name": "C57BL/6N",
      "mgi_strain_acc_id": "MGI:2159965"
    },
    "outcomes_count": 1
  }
}

Plan with a Phenotyping Attempt (phenotyping_attempt_attributes)

{
  "id": 16420,
  "pin": "PIN:000016420",
  "tpn": "TPN:00000001",
  "funder_name": "",
  "work_unit_name": "UCD",
  "is_active": true,
  "status_name": "Production completed",
  "status_dates": [
    {
      "name": "Micro-injection in progress",
      "date": "2014-12-18"
    },
    {
      "name": "Founder obtained",
      "date": "2015-01-06"
    },
    {
      "name": "Chimeras/Founder obtained",
      "date": "2015-01-06"
    },
    {
      "name": "Production complete",
      "date": "2015-02-16"
    }
  ],
  // TODO relation between attempt, outcome, colony
  "comment": null,
  "products_available_for_general_public": true,
  "phenotyping_colony_name": "",
  "type": "phenotyping",
  "attempt_type_name": "phenotyping_attempt",
  "phenotyping_attempt_attributes": {
    "plan_id": 1,
    "imits_phenotype_attempt_id": 1,
    "imits_phenotyping_production_id": 1,
    "phenotyping_experiments_started": "2015-02-16",
    "phenotyping_started": true,
    "phenotyping_complete": true,
    "do_not_count_towards_completeness": false,
    "tissue_distribution_centre_attributes": [
      {
        "id": 1,
        "phenotype_attempt_plan_id": 1,
        "start_date": "2015-02-16",
        "end_date": "2015-02-16",
        "work_unit_name": "UCD",
        "material_type_name": "Embedded tissue"
      }
    ]
  }
}

Outcomes

[
  {
    "id": 1,
    "attempt_id": "",
    "pin": "",
    "allele_attributes": 
    [
      {
        "id": "",
        "name": "",
        "allele_symbol": "",
        "mgi_allele_id": "",
        "allele_type_name": "",
        "allele_subtype_name": "",
        "gene_attributes": 
        [
          {
            "id": "",
            "mgi_accession_id": "MGI:1918645",
            "marker_symbol": "",
            "species_name": "",
            "species_taxon_id": 123
          }
        ],
        "location_attributes": 
        [
          {
            "chr": "",
            "start": "",
            "stop": "",
            "strand": "",
            "genome_build": "",
            "strain_attributes": 
            {
              "name": "C57BL/6N",
              "mgi_strain_acc_id": "MGI:2159965"
            },
            "species_name": "",
            "species_taxon_id": 123,
            "sequence_type": "",
            "chr_feature_type_id": 1    
          }
        ],
        "sequence_attributes": 
        [
        	{
        		"sequence": "",
      			"sequence_type_name" : "",
     			"location_attributes": [
      				{
      					"location_index": "",
      					"chr": "",
     					"start": "",
      					"stop": "",
      					"strand": "",
      					"genome_build": "",
      					"strain_attributes": {
       						"name": "C57BL/6N",
        					"mgi_strain_acc_id": "MGI:2159965"
     					},
      					"species_name": "",
      					"species_taxon_id": 123
      				}
      			]
        	}
        ]
      }
    ],
    "colonies_attributes": 
    [
      {
        "id": 16748,
        "outcome_id": "",
        "name": "GPRRB",
        "genotype_confirmed": true,
        "genotyping_comment": null,
        "is_released_from_genotyping": false,
        "background_strain_attributes": 
        {
          "name": "C57BL/6N",
          "mgi_strain_acc_id": "MGI:2159965"
        },
        "distribution_centres_attributes": 
        [
          {
            "id": 9419,
            "colony_id": "",
            "distribution_network_name": "MMRRC",
            "end_date": null,
            "start_date": "2016-03-30",
            "deposited_material_name": "Frozen sperm",
            "work_unit_name": "UCD",
            "is_distributed_by_emma": false
          }
        ] 
      }
    ],
    "status_name": "Genotype_confirmed",
    "status_dates": [
      {
        "name": "Founder obtained",
        "date": "2015-01-06"
      },
      {
        "name": "Chimeras/Founder obtained",
        "date": "2015-01-06"
      },
      {
        "name": "Genotype_confirmed",
        "date": "2015-02-16"
      }
    ],
    "specimen_attributes":
    [
    	{
    		"specimen_external_ref": "",
    		"property_attributes":
    		[
    			{
    				"name": "",
    				"value": ""
    			}
    		]
    	}
    ]
  }
]
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